Other packages > Find by keyword >

chicane  

Capture Hi-C Analysis Engine
View on CRAN: Click here


Download and install chicane package within the R console
Install from CRAN:
install.packages("chicane")

Install from Github:
library("remotes")
install_github("cran/chicane")

Install by package version:
library("remotes")
install_version("chicane", "0.1.8")



Attach the package and use:
library("chicane")
Maintained by
Syed Haider
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-08-30
Latest Update: 2021-11-06
Description:
Toolkit for processing and calling interactions in capture Hi-C data. Converts BAM files into counts of reads linking restriction fragments, and identifies pairs of fragments that interact more than expected by chance. Significant interactions are identified by comparing the observed read count to the expected background rate from a count regression model.
How to cite:
Syed Haider (2018). chicane: Capture Hi-C Analysis Engine. R package version 0.1.8, https://cran.r-project.org/web/packages/chicane. Accessed 21 Nov. 2024.
Previous versions and publish date:
0.1.0 (2018-08-30 15:20), 0.1.1 (2019-10-01 21:20), 0.1.2 (2020-07-28 01:00), 0.1.3 (2021-01-13 19:20), 0.1.4 (2021-03-24 14:30), 0.1.5 (2021-06-10 09:00), 0.1.6 (2021-07-25 16:50), 0.1.7 (2021-09-21 15:10)
Other packages that cited chicane R package
View chicane citation profile
Other R packages that chicane depends, imports, suggests or enhances
Complete documentation for chicane
Functions, R codes and Examples using the chicane R package
Some associated functions: add.covariates . add.fragment.coordinates . bedtools.installed . bre80 . check.model.numerical.fit . check.split.data.numerical.fit . chicane . combine.replicates . compare.replicates . convert.bam . convert.hicup.digest.bed . convert.standard.format . convert.to.one.based . create.locus.plot . create.modelfit.plot . distance.bin . distance.split . fill.in.zeros . filter.fragments . fit.glm . fit.model . get.combination.count . get.components . get.distance . get.id.components . get.interaction.id . get.trans.counts . is.glm.nb.maxiter.warning . is.glm.nb.theta.error . is.glm.nb.theta.warning . model.rows.sanity.check . model.try.catch . multiple.testing.correct . prepare.data . read.bed . run.model.fitting . smart.split . stratified.enrichment.sample . test.enrichment . verify.interaction.data . 
Some associated R codes: add.covariates.R . add.fragment.coordinates.R . bedtools.installed.R . bre80.R . check.model.numerical.fit.R . check.split.data.numerical.fit.R . chicane-pkg.R . chicane.R . combine.replicates.R . compare.replicates.R . convert.bam.R . convert.hicup.digest.bed.R . convert.standard.format.R . convert.to.one.based.R . create.locus.plot.R . create.modelfit.plot.R . distance.bin.R . distance.split.R . fill.in.zeros.R . filter.fragments.R . fit.glm.R . fit.model.R . get.combination.count.R . get.components.R . get.distance.R . get.id.components.R . get.interaction.id.R . get.trans.counts.R . is.glm.nb.maxiter.warning.R . is.glm.nb.theta.error.R . is.glm.nb.theta.warning.R . model.rows.sanity.check.R . model.try.catch.R . multiple.testing.correct.R . prepare.data.R . read.bed.R . run.model.fitting.R . smart.split.R . stratified.enrichment.sample.R . test.enrichment.R . verify.interaction.data.R .  Full chicane package functions and examples
Downloads during the last 30 days
Get rewarded with contribution points by helping add
Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

SCBiclust  
Identifies Mean, Variance, and Hierarchically Clustered Biclusters
Identifies a bicluster, a submatrix of the data such that the features and observations within the s ...
Download / Learn more Package Citations See dependency  
deductive  
Data Correction and Imputation Using Deductive Methods
Attempt to repair inconsistencies and missing values in data records by using information from vali ...
Download / Learn more Package Citations See dependency  
RcppHNSW  
'Rcpp' Bindings for 'hnswlib', a Library for Approximate Nearest Neighbors
'Hnswlib' is a C++ library for Approximate Nearest Neighbors. This package provides a minimal R int ...
Download / Learn more Package Citations See dependency  
kgschart  
KGS Rank Graph Parser
Restore underlining numeric data from rating history graph of KGS (an online platform of the game o ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  
crossrun  
Joint Distribution of Number of Crossings and Longest Run
Joint distribution of number of crossings and the longest run in a series of independent Bernoulli ...
Download / Learn more Package Citations See dependency  

23,229

R Packages

199,929

Dependencies

62,984

Author Associations

23,230

Publication Badges

© Copyright 2022 - present. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA